LAMMPS (30 Jul 2021) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.5200008 3.5200008 3.5200008 Created orthogonal box = (0.0000000 -39.824263 0.0000000) to (17.244412 39.824263 6.0968202) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7481372 4.9780328 6.0968202 Created 384 atoms using lattice units in orthogonal box = (0.0000000 -39.824263 0.0000000) to (17.244412 39.824263 6.0968202) create_atoms CPU = 0.003 seconds 384 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7481372 4.9780328 6.0968202 Created 396 atoms using lattice units in orthogonal box = (0.0000000 -39.824263 0.0000000) to (17.244412 39.824263 6.0968202) create_atoms CPU = 0.002 seconds 396 atoms in group lower Displacing atoms ... System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 5 21 2 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 776 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/MO_820335782779_000#item-citation The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 5 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.993 | 4.993 | 4.993 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3202.7334 0 -3202.7334 62145.478 116 0 -3430.1641 0 -3430.1641 31960.492 Loop time of 3.44754 on 1 procs for 116 steps with 776 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3202.73344179346 -3430.16082286123 -3430.16410072768 Force two-norm initial, final = 362.10142 0.27915699 Force max component initial, final = 108.56588 0.039839295 Final line search alpha, max atom move = 1.0000000 0.039839295 Iterations, force evaluations = 116 218 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.3737 | 3.3737 | 3.3737 | 0.0 | 97.86 Neigh | 0.019939 | 0.019939 | 0.019939 | 0.0 | 0.58 Comm | 0.030225 | 0.030225 | 0.030225 | 0.0 | 0.88 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02363 | | | 0.69 Nlocal: 776.000 ave 776 max 776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5712.00 ave 5712 max 5712 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 141288.0 ave 141288 max 141288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 141288 Ave neighs/atom = 182.07216 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 5 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 116 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.992 | 4.992 | 4.992 Mbytes Step Temp E_pair E_mol TotEng Press Volume 116 0 -3430.1641 0 -3430.1641 31960.492 8373.9335 132 0 -3432.3822 0 -3432.3822 -141.55445 8507.4877 Loop time of 0.30663 on 1 procs for 16 steps with 776 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3430.16410072769 -3432.38196245533 -3432.3821962491 Force two-norm initial, final = 330.62061 1.6937472 Force max component initial, final = 297.67132 0.91953010 Final line search alpha, max atom move = 0.00064911631 0.00059688199 Iterations, force evaluations = 16 17 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.27655 | 0.27655 | 0.27655 | 0.0 | 90.19 Neigh | 0.019517 | 0.019517 | 0.019517 | 0.0 | 6.37 Comm | 0.0025417 | 0.0025417 | 0.0025417 | 0.0 | 0.83 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008024 | | | 2.62 Nlocal: 776.000 ave 776 max 776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5658.00 ave 5658 max 5658 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 137216.0 ave 137216 max 137216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 137216 Ave neighs/atom = 176.82474 Neighbor list builds = 1 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 5 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.130 | 5.130 | 5.130 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3432.3822 0 -3432.3822 -141.55445 Loop time of 6.334e-06 on 1 procs for 0 steps with 776 atoms 189.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 6.334e-06 | | |100.00 Nlocal: 776.000 ave 776 max 776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5670.00 ave 5670 max 5670 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 137072.0 ave 137072 max 137072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 137072 Ave neighs/atom = 176.63918 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 5 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.130 | 5.130 | 5.130 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -3432.3822 -3432.3822 17.238951 80.85509 6.1035586 -141.55445 -141.55445 -109.14244 -142.15858 -173.36232 2.327323 465.96911 Loop time of 6.876e-06 on 1 procs for 0 steps with 776 atoms 276.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 6.876e-06 | | |100.00 Nlocal: 776.000 ave 776 max 776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5670.00 ave 5670 max 5670 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 68536.0 ave 68536 max 68536 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 137072.0 ave 137072 max 137072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 137072 Ave neighs/atom = 176.63918 Neighbor list builds = 0 Dangerous builds = 0 776 -3432.3821962491 eV 2.32732301996876 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04